Mathematical Biology & Bioinformatics | Volume 17 Issue 2 Year 2022

Brazhnikov E.V., Efimov A.V.

Structure and features of amino acid sequences of Π-modules in OB-folds

Mathematical Biology & Bioinformatics. 2022;17(2):441-451.

doi: 10.17537/2022.17.441.

References

Efimov A.V. Standard structures in proteins. Prog. Biophys. Molec. Biol. 1993;60:201–239. doi: 10.1016/0079-6107(93)90015-C
Efimov A.V. Favoured structural motifs in globular proteins. Structure. 1994;2:999–1002. doi: 10.1016/S0969-2126(94)00102-2
Efimov A.V. Super-secondary structures and modeling of protein folds. Methods Molecular Biology. 2013;932:177-189. doi: 10.1007/978-1-62703-065-6_11
Kargatov A.M., Brazhnikov E.V., Efimov A.V. Structure and features of amino acid sequences of L-modules in SH3-like folds. Molecular Biology. 2018;52(6):929–936. doi: 10.1134/S0026893318060092
Murzin A.G. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 1993;12:861–867. doi: 10.1002/j.1460-2075.1993.tb05726.x
Agrawal V., Kishan K.V. OB-fold: growing bigger with functional consistency. Curr. Protein. Pept. Sci. 2003;4:195–206. doi: 10.2174/1389203033487207
Agrawal V., Kishan K.V. Functional evolution of two subtly different (similar) folds. BMC Struct. Biol. 2001;1:5. doi: 10.1186/1472-6807-1-5
Arcus V. OB-fold domains: a snapshot of the evolution of sequence, structure and function. Curr. Opin. Struct. Biol. 2002;12:794–801. doi: 10.1016/S0959-440X(02)00392-5
Bianco P.R. OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block. Front. Mol. Biosci. 2022;11:784451. doi: 10.3389/fmolb.2022.784451
Nguyen D.D., Kim E.Y., Sang P.B., Chai W. Roles of OB-Fold Proteins in Replication Stress. Front. Cell Dev. Biol. 2020;11. doi: 10.3389/fcell.2020.574466
Bianco P.R. The mechanism of action of the SSB interactome reveals it is the first OB-fold family of genome guardians in prokaryotes. Protein Sci. 2021;30:1757–1775. doi: 10.1002/pro.4140
Efimov A.V. Structure of coiled β-β-hairpins and β-β-corners. FEBS Lett. 1991;284:288–292. doi: 10.1016/0014-5793(91)80706-9
Boshkova E.A., Brazhnikov E.V., Efimov A.V. Relationship between structure and amino acid sequence of strongly twisted and coiled β-hairpins in globular proteins. Mol. Biol. (Mosk.). 2016;50:777−782. doi: 10.7868/S0026898416050049
Efimov A.V. Structural motifs in which β-strands are clipped together with the П-like module. Proteins. 2017;85:1925−1930. doi: 10.1002/prot.25346
Brazhnikov E.V., Kargatov A.M., Efimov A.V. Structure of Looped Regions in β-α- and α-β-Arches in Abcd-Units of Globular Proteins. Mathematical Biology and Bioinformatics. 2016;11:159–169. doi: 10.17537/2016.11.159
Kargatov A.M., Efimov A.V. Unique combinations of βαβ-units and П-like modules in proteins and features of their amino acid sequences. Mol. Biol. (Mosk.). 2018;1:36−41. doi: 10.7868/S002689841801007X
Efimov A.V. Structural trees for proteins containing φ-motifs. Biochemistry (Mosc.). 2008;3:23–28. doi: 10.1134/S0006297908010033
Sternberg M.J., Thornton J.M. On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit. J. Mol. Biol. 1976;105:367–382. doi: 10.1016/0022-2836(76)90099-1
Murzin A.G., Brenner S.E., Hubbard T, Chothia C. SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. J. Mol. Biol. 1995;247:536–540. doi: 10.1006/jmbi.1995.0159
Tatusova T.A., Madden T.L. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 1999;174:247–250. doi: 10.1111/j.1574-6968.1999.tb13575.x
Sayle R.A., Milner-White E.J. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 1995;20:374–376. doi: 10.1016/S0968-0004(00)89080-5
Koradi R., Billeter M., Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 1996;14:51–55. doi: 10.1016/0263-7855(96)00009-4
Efimov A.V. Standard conformations of polypeptide chain in irregular regions of proteins. Mol. Biol. (Mosk.). 1986;20:208–216.
Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997;18:2714–2723. doi: 10.1002/elps.1150181505
Efimov AV. Pseudo-homology of protein standard structures formed by two consecutive β-strands. FEBS Lett. 1987;224:372–376. doi: 10.1016/0014-5793(87)80487-8
Lim V.I. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. J. Mol. Biol. 1974;88:857−872. doi: 10.1016/0022-2836(74)90404-5